There is a growing emphasis, in the fields of drug screening, nucleic acid sequencing and analysis, and protein engineering, on preparing and "reading" high density arrays of chemical or biological species. Such arrays can now be prepared efficiently by massive parallel schemes, such as the selective photomask techniques disclosed in U.S. Pat. No. 5,143,854. Microarrays of this type are typically formed in a planar area of between about 4-100 mm.sup.2, and may have densities of up to several hundred thousand or more distinct array members/cm.sup.2.
In the usual application, the members of the microarrays make up libraries of different-sequence oligonucleotides or polypeptides or small-molecule libraries with different R-group permutations, where each array sequence or permutation is position addressable, i.e., each array position corresponds to a known sequence or permutation.
In use, an array surface is reacted with one or more analytes, such as polynucleotide analytes, receptor proteins, or antiligand molecules, under conditions that promote specific, high-affinity binding of the analyte molecules to one of more of the array members. The goal is to identify one or more position-addressable members of the library array which bind to the analyte, as a method of screening for array compounds which bind to the analyte or, in the case of oligonucleotide arrays, as a method of detecting array members which can hybridize with the analyte molecule(s).
Typically, the analyte is labeled with a detectable reporter such as a fluorescent tag, which in effect can fluorescently label the one or more array regions where analyte binding to the array occurs. In relatively sophisticated schemes, two or more analytes are labeled with distinct fluorescent tags and the extent of analyte binding to the array members can be quantitated according to the level of fluorescence at array binding positions.
A variety of optical scanning devices have been proposed for reading microarrays of this type. U.S. Pat. No. 5,324,633, for example, describes a confocal fluorescence microscope device in which a laser light beam is focused by a lens system onto a small region of a substrate (beam spot less than the area of each array-member region). The same lens system is used to image fluorescence emission from the illuminated region onto a photodetector through a dichroic mirror. An X-Y movable stage functions to position each array region in the substrate successively in the illumination area of the laser beam.
Scanning confocal microscopes designed to correct chromatic aberration that occurs because of the different wavelengths of the illumination beam of fluorescence signal from the sample have also been proposed, e.g., U.S. Pat. Nos. 5,296,700 and 5,260,578. Even with relatively elaborate lens systems, however, scanning confocal microscopes have a number of inherent features that limit sample resolution and the signal-to-noise ratio achievable. The present invention is designed to overcome these limitations.